Relevant bibliographies by topics / Structure-based pharmacophore modeling

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Academic literature on the topic 'Structure-based pharmacophore modeling'

Author: Grafiati
Published: 3 June 2025
Last updated: 31 July 2025

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Journal articles on the topic "Structure-based pharmacophore modeling"

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Mortier, Jérémie, Pratik Dhakal, and Andrea Volkamer. "Truly Target-Focused Pharmacophore Modeling: A Novel Tool for Mapping Intermolecular Surfaces." Molecules 23, no. 8 (2018): 1959. http://dx.doi.org/10.3390/molecules23081959.

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Pharmacophore models are an accurate and minimal tridimensional abstraction of intermolecular interactions between chemical structures, usually derived from a group of molecules or from a ligand-target complex. Only a limited amount of solutions exists to model comprehensive pharmacophores using the information of a particular target structure without knowledge of any binding ligand. In this work, an automated and customable tool for truly target-focused (T²F) pharmacophore modeling is introduced. Key molecular interaction fields of a macromolecular structure are calculated using the AutoGRID
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Kadu, Nilesh S., and Atul V. Ingle. "Three-Dimensional Pharmacophore Modeling of Betulonic Acid Derivatives as a Strong Inhibitor of Human Coronavirus-229E Replication." International Journal of Science and Healthcare Research 6, no. 2 (2021): 356–61. http://dx.doi.org/10.52403/ijshr.20210462.

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These-days, pharmacophore approaches have become one of the foremost tools in drug discovery after the past century’s development. Numerous ligand-based and structure-based strategies are developed for improved pharmacophore modeling with success and extensively applied in virtual screening, de novo design and lead improvement. Till now, there is little information on 3D-pharmacophore studies of 1,2,3-triazolo-fused betulonic acid derivatives as a strong inhibitor for human coronavirus-229E replication. Here, we tend to report the appliance of pharmacophore modeling for betulonic acid derivati
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Mansi, Iman A., Mahmoud A. Al-Sha'er, Nizar M. Mhaidat, Mutasem O. Taha, and Rand Shahin. "Investigation of Binding Characteristics of Phosphoinositide-dependent Kinase-1 (PDK1) Co-crystallized Ligands Through Virtual Pharmacophore Modeling Leading to Novel Anti-PDK1 Hits." Medicinal Chemistry 16, no. 7 (2020): 860–80. http://dx.doi.org/10.2174/1573406415666190724131048.

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Background: 3-Phosphoinositide Dependent Protein Kinase-1 (PDK1) is being lately considered as an attractive and forthcoming anticancer target. A Protein Data Bank (PDB) cocrystallized crystal provides not only rigid theoretical data but also a realistic molecular recognition data that can be explored and used to discover new hits. Objective: This incited us to investigate the co-crystallized ligands' contacts inside the PDK1 binding pocket via a structure-based receptor-ligand pharmacophore generation technique in Discovery Studio 4.5 (DS 4.5). Methods: Accordingly, 35 crystals for PDK1 were
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Simon, A., A. Bencsura, and J. Kardos. "Target Structure-based Modeling of the Glutamate Transporter Pharmacophore." Letters in Drug Design & Discovery 3, no. 5 (2006): 293–97. http://dx.doi.org/10.2174/157018006777574230.

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Kumar, Sivakumar Prasanth, and Prakash Chandra Jha. "Multi-Pharmacophore Modeling of Caspase-3 Inhibitors using Crystal, Dock and Flexible Conformation Schemes." Combinatorial Chemistry & High Throughput Screening 21, no. 1 (2018): 26–40. http://dx.doi.org/10.2174/1386207321666180102114917.

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Aim and Objective: Numerous caspase-3 drug discovery projects were found to have relied on single receptor as the template to recognize most promising small molecule candidates using docking approach. Alternatively, some researchers were contingent upon ligand-based alignment to build up an empirical relationship between ligand functional groups and caspase-3 inhibitory activity quantitatively. To connect both caspase-3 receptor details and its inhibitors chemical functionalities, this study was undertaken to develop receptor- and ligand-pharmacophore models based on different conformational s
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Rayevsky, O. V., O. M. Demchyk, P. A. Karpov та ін. "Structure-based virtual screening for new lead compounds targeted Plasmodium α-tubulin". Faktori eksperimental'noi evolucii organizmiv 28 (31 серпня 2021): 135–39. http://dx.doi.org/10.7124/feeo.v28.1389.

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Aim. Search for new dinitroaniline and phosphorothioamide compounds, capable of selective binding with Plasmodium α-tubulin, affecting its mitotic apparatus. Methods. Structural biology methods of computational prediction of protein-ligand interaction: molecular docking, molecular dynamics and pharmacophore analysis. Selection of compounds based on pharmacophore characteristics and virtual screening results. Results. The protocol and required structural conditions for target (α-tubulin of P. falciparum) preparation and correct modeling of the ligand-protein interaction (docking and virtual scr
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Sugumar, Shobana. "VIRTUAL SCREENING, PHARMACOPHORE MODELING, AND QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIP STUDIES ON HISTAMINE 4 RECEPTOR." Asian Journal of Pharmaceutical and Clinical Research 10, no. 12 (2017): 150. http://dx.doi.org/10.22159/ajpcr.2017.v10i12.19991.

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Objective: To find out novel inhibitors for histamine 4 receptor (H4R), the target for various allergic and inflammatory pathophysiological conditions.Methods: Homology modeling of H4R was performed using easy modeler and validated using structure analysis and verification server, and with the modeled structure, virtual screening, pharmacophore modeling, and quantitative structure activity relationship (QSAR) studies were performed using the Schrodinger 9.3 software.Results: Among all the synthetic and natural ligands, hesperidin, vitexin, and diosmin were found to have the highest dock score,
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Kundu, Sibsankar, and Sangwook Wu. "A Structure Based Study of Selective Inhibition of Factor IXa over Factor Xa." Molecules 26, no. 17 (2021): 5372. http://dx.doi.org/10.3390/molecules26175372.

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Blood coagulation is an essential physiological process for hemostasis; however, abnormal coagulation can lead to various potentially fatal disorders, generally known as thromboembolic disorders, which are a major cause of mortality in the modern world. Recently, the FDA has approved several anticoagulant drugs for Factor Xa (FXa) which work via the common pathway of the coagulation cascade. A main side effect of these drugs is the potential risk for bleeding in patients. Coagulation Factor IXa (FIXa) has recently emerged as the strategic target to ease these risks as it selectively regulates
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Khalaf, Reema A., Dalal Masalha, and Dima Sabbah. "DPP-IV Inhibitory Phenanthridines: Ligand, Structure-Based Design and Synthesis." Current Computer-Aided Drug Design 16, no. 3 (2020): 295–307. http://dx.doi.org/10.2174/1573409915666181211114743.

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Background: Lately, diabetes has become the main health concern for millions of people around the world. Dipeptidyl peptidase-IV (DPP-IV) inhibitors have emerged as a new class of oral antidiabetic agents. Formerly, acridines, N4-sulfonamido-succinamic, phthalamic, acrylic and benzoyl acetic acid derivatives, and sulfamoyl-phenyl acid esters were designed and developed as new DPP-IV inhibitors. Objective: This study aims to develop a pharmacophore model of DPP-IV inhibitors and to evaluate phenanthridines as a novel scaffold for inhibiting DPP-IV enzyme. In addition, to assess their binding in
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Agrawal, Nikhil, Balakumar Chandrasekaran, and Amal Al-Aboudi. "Recent Advances in the In-silico Structure-based and Ligand-based Approaches for the Design and Discovery of Agonists and Antagonists of A2A Adenosine Receptor." Current Pharmaceutical Design 25, no. 7 (2019): 774–82. http://dx.doi.org/10.2174/1381612825666190306162006.

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A2A receptor belongs to the family of GPCRs, which are the most abundant membrane protein family. Studies in the last few decades have shown the therapeutic applications of A2A receptor in various diseases. In the present mini-review, we have discussed the recent progress in the in-silico studies of the A2A receptor. Herein, we described the different structures of A2A receptor, the discovery of new agonists and antagonists using virtualscreening/ docking, pharmacophore modeling, and QSAR based pharmacophore modeling. We have also discussed various molecular dynamics (MD) simulations studies o
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Dissertations / Theses on the topic "Structure-based pharmacophore modeling"

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Berry, Michael. "Massively-Parallel Computational Identification of Novel Broad Spectrum Antivirals to Combat Coronavirus Infection." University of the Western Cape, 2015. http://hdl.handle.net/11394/8321.

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Philosophiae Doctor - PhD<br>Given the significant disease burden caused by human coronaviruses, the discovery of an effective antiviral strategy is paramount, however there is still no effective therapy to combat infection. This thesis details the in silica exploration of ligand libraries to identify candidate lead compounds that, based on multiple criteria, have a high probability of inhibiting the 3 chymotrypsin-like protease (3CUro) of human coronaviruses. Atomistic models of the 3CUro were obtained from the Protein Data Bank or theoretical models were successfully generated by homology m
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Lin, Hsuan-Yu, and 林宣佑. "Structure-based pharmacophore modeling to discover novel CCR5 inhibitors." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/x7cb64.

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碩士<br>國立臺北科技大學<br>化學工程與生物科技系生化與生醫工程碩士班<br>106<br>C-C chemokine receptor type 5 (CCR5), a member of G protein-coupled receptors (GPCRs), not only plays a significant role in inflammatory responses, but also correlates with HIV infection and cancer progression. Recently, blocking of CCR5 was considered as an effective strategy in HIV/cancers therapy. However, only Maraviroc has been approved by FDA in 2007, while the other CCR5 inhibitors were failed in their clinical trials. For searching novel, effective and safe CCR5 inhibitors, a series of computer-aided drug design was performed, including
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Books on the topic "Structure-based pharmacophore modeling"

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Zaheer Ul-Haq and Angela K. Wilson, eds. Frontiers in Computational Chemistry: Volume 6. BENTHAM SCIENCE PUBLISHERS, 2022. http://dx.doi.org/10.2174/97898150368481220601.

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Frontiers in Computational Chemistry presents contemporary research on molecular modeling techniques used in drug discovery and the drug development process: computer aided molecular design, drug discovery and development, lead generation, lead optimization, database management, computer and molecular graphics, and the development of new computational methods or efficient algorithms for the simulation of chemical phenomena including analyses of biological activity. The sixth volume of this series features these six different perspectives on the application of computational chemistry in rationa
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Book chapters on the topic "Structure-based pharmacophore modeling"

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Saddala, Madhu Sudhana, and A. Usha Rani. "Homology Modelling, Structure-Based Pharmacophore Modelling, High-Throughput Virtual Screening and Docking Studies of L-Type Calcium Channel for Cadmium Toxicity." In Translational Bioinformatics and Its Application. Springer Netherlands, 2017. http://dx.doi.org/10.1007/978-94-024-1045-7_7.

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Maji, Siddhartha, Subrat Kumar Pattanayak, Anik Sen, and Vishnu Nayak Badavath. "Pharmacophore modeling in drug design." In Computer Aided Drug Design (CADD): From Ligand-Based Methods to Structure-Based Approaches. Elsevier, 2022. http://dx.doi.org/10.1016/b978-0-323-90608-1.00002-2.

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Pathak, Dharmraj V., Abha Vyas, Hardik G. Bhatt, and Paresh K. Patel. "Pharmacophore Mapping: An Important Tool in Modern Drug Design and Discovery." In Applied Computer-Aided Drug Design: Models and Methods. BENTHAM SCIENCE PUBLISHERS, 2023. http://dx.doi.org/10.2174/9789815179934123010005.

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Computer-Aided Drug Design (CADD) has become an integral part of drug discovery and development efforts in the pharmaceutical and biotechnology industry. Since the 1980s, structure-based design technology has evolved, and today, these techniques are being widely employed and credited for the discovery and design of most of the recent drug products in the market. Pharmacophore-based drug design provides fundamental approach strategies for both structure-based and ligand-based pharmacophore approaches. The different programs and methodologies enable the implementation of more accurate and sophis
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Manhas, Anu, Siddhi Kediya, and Prakash C. Jha. "Pharmacophore Modeling Approach in Drug Discovery Against the Tropical Infectious Disease Malaria." In Frontiers in Computational Chemistry: Volume 6. BENTHAM SCIENCE PUBLISHERS, 2022. http://dx.doi.org/10.2174/9789815036848122060006.

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In recent years, the world has faced several outbreaks caused by viral diseases, resulting in deaths and comorbidities, harming the health of the population. Due to the “constant” discovery of new antivirals, vaccines, hygiene habits, and basic sanitation, society had the false impression of being free from these diseases. However, since the 1980s, various outbreaks have occurred, such as HIV (Human immunodeficiency virus) and recently, ZIKV (Zika virus), CHIKV (Chikungunya virus), and EBOV (Ebola virus) have increased the concern about such pathogens, resulting in advances in drug discovery.
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de Medeiros e Silva, Yvnni Maria Sales, Marianny de Souza, Daniel Calazans Medeiros, et al. "Current Trends in Molecular Modeling to Discover New Anti-inflammatory Drugs Targeting mPGES1." In Frontiers in Computational Chemistry volume 7. BENTHAM SCIENCE PUBLISHERS, 2024. http://dx.doi.org/10.2174/97898151790331240700007.

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Inflammation is a natural response to external stimuli related to the protection of the organism. However, their exaggerated reaction can cause severe damage to the body and is related to several diseases, including allergies, rheumatoid arthritis, diabetes, cancer, and various infections. Furthermore, inflammation is mainly characterized by increased temperature, pain, flushing, and edema due to the production of pro-inflammatory cytokines, such as prostaglandins, and can be controlled using anti-inflammatory drugs. In this sense, selective prostaglandin E2 (PGE2 ) inhibition has been targete
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Chauhan, Arushi, and Pramod K. Avti. "Computational Approaches in Evaluating the 5-HT Subtype Receptor Mechanism of Action for Developing Novel Chemical Entities." In Frontiers in Computational Chemistry volume 7. BENTHAM SCIENCE PUBLISHERS, 2024. http://dx.doi.org/10.2174/9789815179033124070006.

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The G-protein coupled receptor GPCR family is the most numerous and diversified set of membrane receptors linked with various neurological disorders like Epilepsy, Alzheimer's disease, Fronto-temporal dementia, Vascular dementia, Parkinson's disease, and Huntington's disease. They provide messages to the cell by interacting with various ligands, which include hormones, neurotransmitters, and photons. They are the focus of roughly one-third of the medications on the market today. Similarly, the subtype of the serotonin receptor, 5-hydroxytryptamine 2B (5-HT2B), belongs to the G-protein receptor
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Puratchikody, A., A. Umamaheswari, Navabshan Irfan, and Dharmaraj Sriram. "Molecular Modelling Studies of Novel COX-2 Inhibitors." In Advances in Medical Technologies and Clinical Practice. IGI Global, 2019. http://dx.doi.org/10.4018/978-1-5225-7326-5.ch008.

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Molecular modelling uses theoretical and computational chemistry, which offers insight into the nature of molecular systems. This chapter highlights the theoretical explanation of molecular modelling methods and describes the designing of novel tyrosine COX-2 inhibitors using molecular modelling as an example. As a first step, fragment-based drug design is used to design the novel tyrosine analogues and ligand-based drug design such as QSAR, and pharmacophore was used to identify the descriptors, ensemble of steric and electronic features, which is responsible for the selective COX-2 inhibitio
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K. Kwofie, Samuel, Gabriel B. Kwarko, Emmanuel Broni, Michael B. Adinortey, and Michael D. Wilson. "Molecular Informatics of Trypanothione Reductase of Leishmania major Reveals Novel Chromen-2-One Analogues as Potential Leishmanicides." In Leishmaniasis - General Aspects of a Stigmatized Disease. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.100594.

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Trypanothione reductase (TR), a flavoprotein oxidoreductase is an important therapeutic target for leishmaniasis. Ligand-based pharmacophore modelling and molecular docking were used to predict selective inhibitors against TR. Homology modelling was employed to generate a three-dimensional structure of Leishmania major trypanothione reductase (LmTR). A pharmacophore model used to screen a natural compound library generated 42 hits, which were docked against the LmTR protein. Compounds with lower binding energies were evaluated via in silico pharmacological profiling and bioactivity. Four compo
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Akisheva, Alina, and Iryna Valivodz. "DOCKING ANALYSIS OF THE INTERACTION OF PROPOXAZEPAM WITH BIOTARGETS THAT REGULATE ITS MECHANISM OF ACTION AND PHARMACOLOGICAL ACTIVITY." In Science, technology and innovation in the modern world. Publishing House “Baltija Publishing”, 2023. http://dx.doi.org/10.30525/978-9934-26-364-4-7.

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One of 1.4-benzodiazepine 3-alcoxy derivatives – propoxazepam, possessing high analgetic action, also effectively suppresses experimental seizures of different etiology. Unexpected combination of pharmacological spectrum components suggests its different binding sites of GABAA receptor subunits.The aim of the work was docking analysis of the interaction of Propoxazepam with biotargets that mediate its mechanism of action and pharmacological activity (using experimental data of the propoxazepam conformation and calculated data for the three-dimensional structure of the ligand-binding site and s
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